RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9436
(188 letters)
>gnl|CDD|240253 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
Length = 202
Score = 104 bits (262), Expect = 2e-28
Identities = 41/79 (51%), Positives = 55/79 (69%)
Query: 64 SMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEV 123
M PHK RGA ALKRLKV+EG+P Y + +R+ +P+ALR + LKP R Y +G +S V
Sbjct: 85 GMLPHKTKRGAAALKRLKVFEGVPAPYDKVKRVVIPSALRVLRLKPERPYTVLGDLSAHV 144
Query: 124 GWKYKTIVRHLERKRREKS 142
GWKY +V LE KR+E++
Sbjct: 145 GWKYADVVAKLEEKRKERA 163
>gnl|CDD|162192 TIGR01077, L13_A_E, ribosomal protein L13, archaeal/eukaryotic.
This model represents ribosomal protein of L13 from the
Archaea and from the eukaryotic cytosol. Bacterial and
organellar forms are represented by model TIGR01066
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 142
Score = 70.5 bits (173), Expect = 6e-16
Identities = 31/63 (49%), Positives = 42/63 (66%), Gaps = 1/63 (1%)
Query: 65 MTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEVG 124
M PHK RG AL+RLKVY GIPP+ +++R+ VP AL L P R Y ++G ++ +G
Sbjct: 81 MLPHKTARGRAALRRLKVYVGIPPELDKKKRVVVPEAL-VSRLSPTRKYVTLGELAKFLG 139
Query: 125 WKY 127
WKY
Sbjct: 140 WKY 142
>gnl|CDD|235793 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
Length = 146
Score = 43.3 bits (103), Expect = 1e-05
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 65 MTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEVG 124
M P+K RG +ALKRLKVY G+P + ++ + A + Y ++G +S E+G
Sbjct: 86 MLPYKKPRGREALKRLKVYVGVPKELEGKEFEVIDEAD--LSRLSTIKYVTLGEVSKELG 143
Query: 125 WKY 127
K+
Sbjct: 144 AKF 146
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 35.7 bits (83), Expect = 0.004
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 65 MTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRT 104
M P G ALKRLKVY GIP + ++ P AL
Sbjct: 109 MLPKN-PLGRAALKRLKVYAGIPHPHEAQK----PEALEL 143
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 34.8 bits (81), Expect = 0.006
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 65 MTPHKLDRGAKALKRLKVYEGIPPKYARRQR 95
M P G ALKRLKVY G P +A ++
Sbjct: 94 MLPKNK-LGRAALKRLKVYAGSPHPHAAQKP 123
>gnl|CDD|238230 cd00392, Ribosomal_L13, Ribosomal protein L13. Protein L13, a
large ribosomal subunit protein, is one of five proteins
required for an early folding intermediate of 23S rRNA
in the assembly of the large subunit. L13 is situated on
the bottom of the large subunit, near the polypeptide
exit site. It interacts with proteins L3 and L6, and
forms an extensive network of interactions with 23S
rRNA. L13 has been identified as a homolog of the human
breast basic conserved protein 1 (BBC1), a protein
identified through its increased expression in breast
cancer. L13 expression is also upregulated in a variety
of human gastrointestinal cancers, suggesting it may
play a role in the etiology of a variety of human
malignancies.
Length = 114
Score = 28.6 bits (65), Expect = 0.79
Identities = 14/22 (63%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 65 MTPHKLDRGAKALKRLKVYEGI 86
M P K G ALKRLKVYEG
Sbjct: 94 MLP-KNKLGRAALKRLKVYEGA 114
>gnl|CDD|224049 COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport
system, ATPase component [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 252
Score = 28.4 bits (64), Expect = 1.8
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 13/58 (22%)
Query: 62 SESMTPHKLDRGAKALKRLKVYEGIPPKYARR----------QRLCVPTALRTVCLKP 109
SE + PH L + + + L G+PP + R QR+ + R + +P
Sbjct: 106 SEPLRPHGLSKSQQRIAELLDQVGLPPSFLDRRPHELSGGQRQRIAI---ARALIPEP 160
>gnl|CDD|169269 PRK08192, PRK08192, aspartate carbamoyltransferase; Provisional.
Length = 338
Score = 28.2 bits (63), Expect = 3.1
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 5/44 (11%)
Query: 42 SKIRAVEKLELFSIENARNQSESMTPHKLDRGAKALKRLKVYEG 85
S I +V +L+ +I+ N ++ M P+ L KR +V EG
Sbjct: 6 SHILSVNQLDRDAIQRIFNVADRMEPYALRE-----KRTRVLEG 44
>gnl|CDD|236341 PRK08850, PRK08850, 2-octaprenyl-6-methoxyphenol hydroxylase;
Validated.
Length = 405
Score = 27.8 bits (62), Expect = 3.9
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 5 ALSIEDTRLATLVTEKTTSTKRNIGHFDRKRKQARHESKIRAVEKL-ELFSIEN 57
A S+ LA + KRN+ ++R RK A I A++ +LFS N
Sbjct: 309 AASLAQEILALWQQGRDIGLKRNLRGYERWRK-AEAAKMIAAMQGFRDLFSGSN 361
>gnl|CDD|239384 cd03110, Fer4_NifH_child, This protein family's function is unkown.
It contains nucleotide binding site. It uses NTP as
energy source to transfer electron or ion.
Length = 179
Score = 26.1 bits (58), Expect = 9.1
Identities = 15/50 (30%), Positives = 19/50 (38%), Gaps = 15/50 (30%)
Query: 7 SIEDTRLATLVTEKTTSTKRNIGHFDRKRKQARHESKIRAVEKLELFSIE 56
S+ A LVTE T S H+ + RAVE + F I
Sbjct: 111 SLTGADAALLVTEPTPS--------------GLHDLE-RAVELVRHFGIP 145
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.132 0.382
Gapped
Lambda K H
0.267 0.0766 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,073,358
Number of extensions: 805263
Number of successful extensions: 686
Number of sequences better than 10.0: 1
Number of HSP's gapped: 685
Number of HSP's successfully gapped: 34
Length of query: 188
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 97
Effective length of database: 6,901,388
Effective search space: 669434636
Effective search space used: 669434636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.3 bits)